The effect of a silicon substrate surface pretreatment on epitaxial iron silicide film formation on a Si(100) substrate with ion beam sputter deposition (IBSD) was investigated. In this study, two surface pretreatment methods namely, thermal etching (TE) and sputter etching (SE) with subsequent thermal annealing, were employed. The interface structure between a -FeSi 2 film and a Si substrate was analyzed by cross-sectional observation using a transmission electron microscope (XTEM). Highresolution XTEM images showed that the lattice of the Si substrate is an almost perfect crystal immediately after the TE treatment. However, the TE treatment results in an undulated interface, and the deposited silicide contained coalesced -FeSi 2 islands. On the other hand, the dislocations and stacking faults produced by radiation damage were observed near the Si substrate surface for the SE treatment. Even though this treatment produced defects, the interface of the SE-treated epitaxial -FeSi 2 (100) film had a smooth interface after the deposition at 973 K. It can be concluded that a moderate disorder of the silicon substrate surface treated by SE may well enhance the mixing of Fe and Si atoms for the epitaxial growth of -FeSi 2 .